"He will be taken from this place (Central Court) to Western Australia in the custody of Australian Federal Police," Magistrate Maloney said.

The court heard Heydarkhani needs "medical attention" for a mental health issue, and he will be allowed to take his required medication.

He will appear in Perth Magistrate's Court at the first opportunity.

Home Affairs Minister Brendan O'Connor announced the arrest of the 40-year-old Iranian man today.

"I can confirm that early this morning Indonesia deported a 40-year-old Iranian-born Australian citizen to Australia," he told reporters in Canberra.

The man arrived in Sydney at 10am and was immediately arrested by Australian authorities.

"He was arrested by the Australian Federal Police for alleged facilitation of the people smuggling venture that led to the tragedy on Christmas Island on the 15th of December last year," Mr O'Connor said.

The charges relate to the Christmas Island boat tragedy and three other people smuggling ventures.

Four of the offences carry penalties of up to 20 years imprisonment each.

It's believed 48 men, women and children died in the Christmas Island capsize when their wooden boat smashed against the rocky shore in appalling conditions on the island off Western Australia.

Only 42 survived.

Mr O'Connor said Indonesia was aware Australia was interested in the arrested man.

"People have to understand that if they engage in the terrible crime of people smuggling, Australia law enforcement agencies and their police partners in the region will do everything they can to frustrate, prosecute and punish those who seek to make a profit by endangering the lives of others," he said.

"Those people who seek to lure, in some cases people who are desperate, into unseaworthy vessels where people's lives are at risk, where people perish, will be punished."

Mr O'Connor said an overwhelming number of the 89 charges related to the Christmas Island boat tragedy in December.

But he refused to say when Australia first sought the man's extradition.

Indonesia was in a position to deport him now because he'd overstayed his visa, the minister said.

Australian authorities would seek to extradite the 40-year-old to Western Australia to face court.

The most serious charges were aggravated people smuggling offences.

"It's clear after the Malaysian government and then the Indonesian government have (recently) enacted laws for the first time criminalising people smuggling that the region is taking this very seriously," Mr O'Connor said.

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